crossing96/oncoscreening huggingface dataset:
A novel risk score based on a combined signature of 10 immune system genes to predict bladder cancer prognosis.	Bladder cancer (BC) is a common internal malignant tumor with a poor prognosis worldwide. There is an urgent need to better understand the pathogenesis and progression of BC and to find useful biomarkers for diagnosis and prognosis. This study was aimed at developing a potential immunogenomic prognostic signature for BC patients. To identify possible immune-system-related genes (IRGs) whose parameters predict the survival of BC patients, we chose 371 BC patients and analyzed differentially expressed IRGs from The Cancer Genome Atlas (TCGA) datasets. We then derived a 10-IRG formula, including MMP9, RBP7, PDGFRA, AHNAK, OAS1, OLR1, RAC3, SLIT2, IGF1, and AGTR1, to estimate BC prognosis. To validate the mRNA levels of these IRGs, we performed quantitative PCR and found that the expression of these genes almost matched the corresponding mRNA expression levels in TCGA. Furthermore, we validated the prognostic value of the new risk model using two external datasets from Gene Expression Omnibus: GSE13507 (n = 165) and GSE32894 (n = 224). Our data pointed to a significant correlation between the risk model and patients' prognosis. Bioinformatic analysis revealed that products of the IRGs have possible effects on tumor immune processes such as an inflammatory response and cytokine-cytokine receptor interaction. Finally, assessment of the clinical value of the immune-system-based risk signature showed that several of these IRGs were differentially expressed between patients with different clinical characteristics: a high risk score positively correlated with female sex, advanced tumor stage, more advanced T stage, and lymph node metastasis. This immunogenomic signature may represents a reliable prognostic tool for BC and can help to design an individualized immunotherapy.	bladder
Practicability of clinical application of bladder cancer molecular classification and additional value of epithelial-to-mesenchymal transition: prognostic value of vimentin expression.	BACKGROUND: Bladder cancer (BlCa) taxonomy has proved its impact in patient outcome and selection for targeted therapies, but such transcriptomic-based classification has not yet translated to routine practice. Moreover, epithelial-to-mesenchymal transition (EMT) has shown relevance in acquisition of more aggressive BlCa phenotype. We aimed to test the usefulness of the molecular classification, as defined by immunohistochemistry (a routinely performed and easy-to-implement technique), in a well-defined BlCa cohort of both non-muscle invasive (NMIBC) and muscle invasive (MIBC) disease. Also, we aimed to assess the additional prognostic value of the mesenchymal marker vimentin to the stratification strategy. METHODS: A total of 186 samples were available. Immunohistochemistry/RT-qPCR for luminal markers GATA3/FOXA1, basal markers KRT5/KRT6A and vimentin were performed. RESULTS: mRNA expression levels of the markers positively correlated with immunoexpression scores. We found substantial overlapping in immunoexpression of luminal and basal markers, evidencing tumor heterogeneity. In MIBC, basal tumors developed recurrence more frequently. NMIBC patients with higher vimentin immunoexpression endured poorer disease-free survival, and increased expression was observed from normal bladder-NMIBC-MIBC-metastases. CONCLUSIONS: The classification has the potential to be implemented in routine, but further adjustments in practical scoring should be defined; focusing on additional markers, including those related to EMT, may further refine BlCa molecular taxonomy.	bladder
Combination therapy in advanced urothelial cancer: the role of PARP, HER-2 and mTOR inhibitors.	INTRODUCTION: Despite significant advances in the treatment of metastatic urothelial carcinoma, including the advent of immune checkpoint inhibitors, this disease is still challenging to treat and associated poor outcomes remain. Genomic characterization of advanced-stage urothelial carcinoma is widening the field of potential treatments due to the identification of novel biologic drivers. AREAS COVERED: In this review, we explore the role of PARP, HER-2, and mTOR inhibitors in the therapeutic scenario of advanced urothelial carcinoma, as these pathways are frequently altered in urothelial carcinoma. We report ongoing clinical trials involving these agents, either in monotherapy or in combination with other compounds, highlighting the dynamic scenario of metastatic urothelial carcinoma treatment. EXPERT OPINION: Several challenges need to be faced in the development of new potential therapeutic strategies, such as inter/intratumoral heterogeneity and the lack of validated biomarkers.	bladder
VI-RADS: Multiinstitutional Multireader Diagnostic Accuracy and Interobserver Agreement Study.	BACKGROUND. The Vesical Imaging Reporting and Data System (VI-RADS), based on multiparametric MRI (mpMRI), was developed to provide accurate information for the diagnosis of muscle-invasive bladder cancer (MIBC). OBJECTIVE. The purpose of our study was to evaluate the interobserver agreement and diagnostic performance of VI-RADS among readers with different levels of experience. METHODS. This retrospective study included 91 consecutive patients who underwent mpMRI before transurethral resection of bladder tumor (TURBT) from July 2010 through August 2018. After attending a training session, seven radiologists (five radiologists experienced in bladder MRI and two inexperienced radiologists) reviewed and scored all MRI examinations according to VI-RADS. The interobserver agreement was assessed by kappa statistics. ROC analysis was used to evaluate the diagnostic performance for MIBC. AUCs were estimated. RESULTS. Among 91 patients (72 men and 19 women; mean age ± SD, 73.2 ± 10.2 years), 48 (52.7%) had MIBC and 43 (47.3%) had non-muscle-invasive bladder cancer. Sixty-eight patients were treated with TURBT, and 23 were treated with radical cystectomy. Interobserver agreement was moderate to substantial (κ = 0.60-0.80) among the experienced readers, substantial (κ = 0.67) between the two inexperienced readers, and moderate to substantial (κ = 0.55-0.75) between the experienced and inexperienced readers. The pooled AUC was 0.88 (range, 0.82-0.91) for experienced readers and 0.84 (range, 0.83-0.85) for inexperienced readers, and 0.87 for all readers. Using a VI-RADS score of 4 or greater as the cutoff value for MIBC, the pooled sensitivity and specificity were 74.1% (range, 66.0-80.9%) and 94.1% (range, 88.6-97.7%) for experienced readers and 63.9% (range, 59.6-68.1%) and 86.4% (range, 84.1-88.6%) for inexperienced readers. Using a VI-RADS score of 3 or greater as the cutoff value, the pooled sensitivity and specificity were 83.4% (range, 80.9-85.1%) and 77.3% (range, 61.4-88.6%) for experienced readers and 82.0% (range, 80.9-83.0%) and 73.9% (range, 72.7-75.0%) for inexperienced readers. CONCLUSION. We observed moderate to substantial interobserver agreement and a pooled AUC of 0.87 among radiologists of different levels of expertise using VI-RADS. CLINICAL IMPACT. VI-RADS could help determine the depth and range of excision in TURBT, decreasing the risk of complications and enhancing the accuracy of pathologic diagnosis.	bladder
Bioinformatic identification of prognostic indicators in bladder cancer.	Aim: Bladder cancer (BC) is one of the most common malignancies with poor prognosis. We aimed to identify a genetic signature for predicting the prognosis of BC. Materials & methods: Kaplan-Meier survival and Cox regression analyses were used to construct a prognostic signature using data from The Cancer Genome Atlas. Results: Fifty four upregulated and 47 downregulated immune-related genes (IRGs) were identified in BC. A prognostic signature based on the expression of five IRGs was determined, which was moderately accurate in the prognosis of tumors. The prognostic signature was correlated with tumor stage, tumor burden and lymph node metastasis. The expression of IRGs were associated with immune infiltration. Conclusion: We determined a five gene signature, which correlates with the prognosis of BC patients, providing additional information for effective treatment.	bladder
The relation between the ghrelin receptor and FOXP3 in bladder cancer.	Immune responses play an important role in the fate of bladder cancer tumors. Treg cells are immunosuppressive and down-regulate the proliferation of effector T cells, which favor tumor survival. Ghrelin is a hormone that stimulates release of growth hormone and anti-inflammatory response to cancer cells. Ghrelin also is a gastrointestinal hormone that regulates immune responses via the growth hormone secretagogue receptor (GHS-R1a). The relation among ghrelin, its receptor, and Treg cells that surround bladder tumors is not clear. We found that Foxp3(+) T and GHS-R1a cells are increased significantly in bladder tumor tissues. Therefore, we suggest that ghrelin may increase the number of Treg cells in the tumor and suppress activity of the immune system against bladder cancer.	bladder
The Feasibility and Impact of a Presurgical Exercise Intervention Program (Prehabilitation) for Patients Undergoing Cystectomy for Bladder Cancer.	OBJECTIVE: To assess the feasibility of a prehabilitation program for cystectomy patients and to determine the effectiveness of the program in improving strength and functional capacity in the peri-operative period. MATERIALS AND METHODS: This phase I/II study accrued patients ≥60 years old from January 2013 to October 2017 with biopsy-proven bladder cancer, Karnofsky performance score ≥70 and a sedentary baseline lifestyle to participate in a 4-week supervised preoperative exercise training program. Primary outcomes were feasibility and safety; secondary outcomes included changes in fitness, patient-reported QOL, peri-operative complications and readmissions. Student's ttests and Wilcoxon signed-rank test were performed. RESULTS: Fifty-four patients enrolled in the program. Successful completion, defined as patients who began the program and adhered to >70% of the sessions, was attained by 41 of 51 patients (80.4%, 90% CI [71%-90%]). There were no adverse events. Fitness and patient-reported QOL improved postintervention, with sustained improvements in general and mental health 90-days postsurgery. The primary limitation is no control group. CONCLUSION: Prehabilitation prior to cystectomy is feasible, safe, and results in improvements in patient strength, endurance and sustained improvements in patient-reported QOL from baseline. Efforts to further evaluate the impact of prehabilitation in this population in an expanded and randomized fashion are warranted.	bladder
Impact of tumor size on the oncological outcome of high-grade nonmuscle invasive bladder cancer - examining the utility of classifying Ta bladder cancer based on size.	PURPOSE: To examine survival rates and to calculate the risk of disease recurrence, progression, overall, and cancer-specific mortality in patients diagnosed with high-risk NMIBC using a multi-institutional dataset to evaluate differences between the guidelines of the European Association of Urology and the guidelines of the National Comprehensive Cancer Network (NCCN) with regard to tumor size in risk stratification. METHODS AND MATERIAL: In total 1,116 individuals diagnosed with high-risk NMIBC between 2001 and 2013 were included in the analysis. Patients were stratified to NCCN guideline recommendations (high-grade T1, high-grade Ta ≤ 3 cm, and high-grade Ta > 3 cm). Recurrence and progression rates were calculated. Kaplan-Meier curves were fitted to examine differences in recurrence-free (RFS) and progression-free survival (PFS). Multivariable Cox proportional hazards regression models were employed to calculate differences in the RFS, PFS, overall, and cancer-specific survival (CSS). RESULTS: The majority of patients were diagnosed with high-grade T1 disease (N = 576, 51.6%), while 34.2% and 14.2% of patients were diagnosed with high-grade Ta ≤ 3 cm and Ta > 3 cm NMIBC, respectively. The 1- and 5-year RFS (1-year: 80.5% vs. 64.9%; 5-year: 58.6% vs. 48.3%, P = 0.048) and PFS (1-year: 99.1% vs. 98.6%; 5-year: 97.7% vs. 92.4%, P = 0.054) rates were higher in patients with Ta ≤ 3 cm. Patients diagnosed with high-grade Ta > 3 cm experienced unfavorable progression-free, and cancer-specific survival compared to high-grade Ta ≤ 3 cm, respectively (PFS: 2.41, 95% confidence interval [CI] 1.05-5.56, P = 0.038; CSS: hazard ratios [HR] 2.22, 95% CI 1.02-4.89, P = 0.048). CONCLUSION: Patients diagnosed with high-grade Ta NMIBC ≤3 cm demonstrated a favorable progression-free, and cancer-specific survival compared to patients diagnosed with high-grade Ta > 3 cm and high-grade T1 NMIBC.	bladder
Catechol-Functionalized Alginate Nanoparticles as Mucoadhesive Carriers for Intravesical Chemotherapy.	This research aimed to synthesize and evaluate mucoadhesive catechol-functionalized alginate (Cat-Alg) nanoparticles (NPs) for bladder cancer. Cat-Alg was synthesized using coupling chemistry, and the structure was verified using NMR and FT-IR. Cat-Alg NPs were generated by ionic gelation between the synthesized Cat-Alg and calcium chloride. Garcinia mangostana L. extract (GM extract) was entrapped into the NPs during particle formation. The physical characteristics, mucoadhesive properties, drug loading and release, cellular uptake, and anticancer activity of the GM extract-loaded NPs were investigated. The Cat-Alg NPs were spherical with sizes in the range of 155-186 nm. The slightly negative surface charge of the NPs provided them with excellent stability. The Cat-Alg NPs could be retained on a porcine bladder mucosa to a greater extent compared with unmodified Alg NPs. High loading efficiency (71.6%) and loading capacity (292 μg/mg) of GM extract in the NPs were achieved, and a constant release of GM extract was obtained for up to 8 h with zero-order kinetics. Moreover, the GM extract-loaded NPs were deposited in bladder tissue and accumulated in MB49 cells at a higher rate compared with GM extract suspension. In addition, the NPs could kill a mouse urothelial carcinoma cell line with low IC(50). Therefore, these NPs have the potential to be a mucoadhesive drug delivery system for bladder cancer treatment. However, additional in vivo investigations are needed for clinical application in cancer treatment. Graphical abstract.	bladder
Bladder cancer in patients younger than 40 years: outcomes from the National Cancer Database.	PURPOSE: To evaluate the clinical, pathological, and survival outcomes of bladder cancer in patients aged 18-40 years. METHODS: We identified 362,091 bladder cancer patients from the National Cancer Database between 2004-2013 and compared patients aged 18-40 years to those > 40 years of age with univariate analysis using Chi-square tests. A subset analysis was performed on patients who underwent cystectomy. Multivariable Cox regression was used for overall survival analysis. RESULTS: Our final analysis included 314,177 patients with 3314 (1.1%) patients aged 18-40 years. Patients aged 18-40 years had a lower male-to-female ratio (2.4 versus 3.0), a greater proportion of low-grade tumors (72.7% versus 48.3%, p < 0.001), non-muscle invasive tumors (90.3% versus 81.2%, p < 0.001), and variant histology (4.0% versus 3.3%, p < 0.001). Similar trends were observed at cystectomy including lower male-to-female ratio in the 18-40 years group (1.7 versus 3.1), a greater proportion of variant histology (25.0% versus 10.0%, p < 0.001); and 53.3% of those younger patients with variant histology were women. Patients aged 18-40 years who underwent cystectomy had a higher proportion of locally advanced disease (pT4 19.2% versus 14.6%, p = 0.004). Multivariable analyses in both cohorts demonstrated that variant histology was a predictor of worse overall survival. CONCLUSION: The majority of patients aged 18-40 years with bladder cancer present with low-grade, non-muscle-invasive disease associated with better survival. However, a subset of younger patients with a higher proportion of women presents with aggressive bladder cancer which may be partly explained by a higher prevalence of variant histology.	bladder
Re-establishing the Role of Robot-assisted Radical Cystectomy After the 2020 EAU Muscle-invasive and Metastatic Bladder Cancer Guideline Panel Recommendations.	The EAU guidelines panel on muscle-invasive and metastatic bladder cancer (MIBC) recently recommended open radical cystectomy (ORC) as the best surgical approach for MIBC patients. We critically re-examine the indications for considering ORC as the first choice over robot-assisted radical cystectomy. To the best of our knowledge, this is not supported by trials or meta-analyses.	bladder
Does Xylinas' nomogram accurately predict intravesical recurrence risk after radical nephroureterectomy for primary upper urinary tract urothelial carcinoma when applied to Asian populations?	OBJECTIVE: To validate a prognostic nomogram (Xylinas' nomogram) for intravesical recurrence after radical nephroureterectomy for primary upper urinary tract urothelial carcinoma patients of Asian descent. METHODS: Clinicopathological and survival data from 243 primary urinary tract urothelial carcinoma patients who underwent radical nephroureterectomy with bladder cuff excision between January 2004 and May 2017 were collated. Univariate and multivariable Cox regression analyses were performed to identify independent risk factors associated with intravesical recurrence-free survival. External validation was determined using regression coefficients abstracted from previously published data. Performance was then quantified through calibration and discrimination, according to concordance indexes (c-index) in receiver operating characteristic curves. RESULTS: 163 patients met our eligibility criteria and were finally included in this study. At a median follow-up of 60 months, intravesical recurrence occurred in 29.4% (n = 48). Multivariable analysis revealed that being male, ureteral tumor location, tumor multifocality and previous bladder cancer were independent prognostic factors of intravesical recurrence-free survival. When Xylinas' nomogram was applied to our cohort, the discriminatory power was found to be roughly equivalent with a c-index of 68.3% for the reduced model and 68.4% for the full model. Calibration plots also revealed intravesical recurrence predictions at 3, 6, 12, 18, 24 and 36 months had relative concordance. Contrasting the respective performances of the reduced and full model suggests there is no significant difference between the two (all P > 0.05). CONCLUSIONS: This nomogram appears accurate at predicting intravesical recurrence after radical nephroureterectomy for primary urinary tract urothelial carcinoma in Asian populations. However, it remains necessary to data mine for unknown prognostic factors for optimization. Further external validation is required across larger, ethically diverse populations before applying this nomogram in clinical practice.	bladder
Bladder cancer in Ireland: a 21-year review.	INTRODUCTION: Bladder carcinoma is one of the most commonly diagnosed cancers worldwide; however, various studies have reported on marked international variation in incidence and mortality rates. The aim of this study was to report national figures on incidence, survival and risk factors of bladder cancer. This retrospective review is the first to offer a comprehensive analysis of incidence rates, mortality and potential risk factors in the Irish population from 1994 to 2015. METHODS: This was a retrospective study of incidence and survival trends in bladder cancer in the Irish population from 1994 to 2014 based on data from the National Cancer Registry of Ireland (NCRI). Patient demographics, pathology and survival data, as well as potential contributing factors, were studied. RESULTS: A total of 9656 cases of bladder cancer were diagnosed from 1994 to 2015, with majority of cases occurring in males (71%). Survival decreased with increasing age, higher grade and higher stage. Bladder cancer is more common in those with a smoking history and with a higher deprivation score. Urothelial cell carcinoma was the most common pathology (95%), with the majority of patients being stage 1 or 2 (44.7%). CONCLUSION: The overall incidence of bladder cancer in Ireland has fallen, in line with reducing smoking rates. Our data reflects international trends in incidence, survival and contributing risk factors.	bladder
Adjuvant chemotherapy is ineffective in patients with bladder cancer and variant histology treated with radical cystectomy with curative intent.	OBJECTIVES: Adjuvant chemotherapy (ACT) is recommended for non-organ-confined bladder cancer (BCa) after radical cystectomy (RC) and pelvic lymph node dissection (PLND), but there are sparse data regarding its specific efficacy in patients with histological variants. The aim of our study was to evaluate the role of ACT on survival outcomes in patients with variant histology in a large multicenter cohort. MATERIALS AND METHODS: We retrospectively evaluated data of 3963 patients with BCa treated with RC and bilateral PLND with curative intent at several institutions between 1999 and 2018. The histological type was classified into six groups: pure urothelial carcinoma (PUC) or squamous, sarcomatoid, micropapillary, glandular and neuroendocrine differentiation. Multivariable competing risk analysis was applied to assess the role of ACT on recurrence and cancer-specific mortality (CSM) in each histological subtype. RESULTS: Of the 3963 patients included in the study, 23% had variant histology at RC specimen and 723 (18%) patients received ACT. ACT was found to be significantly associated with reduced risk of recurrence (sub-hazard ratio [SHR]: 0.55, confidence interval [CI] 0.42-0.71, p < 0.001) and CSM (SHR: 0.58, CI 0.44-0.78, p < 0.001) in the PUC only, while no histological subtype received a significant benefit on survival outcomes (all p > 0.05) from administration of ACT. The limitation of the study includes the retrospective design, the lack of a central pathology review and the number of ACT cycles. CONCLUSION: In our study, the administration of ACT was associated with improved survival outcomes in PUC only. No histological subtype found a benefit in overall recurrence and CSM from ACT.	bladder
Implementation of ERAS (Enhanced Recovery After Surgery) protocols for radical cystectomy patients: The pathway to standardization. A systematic review.	CONTEXT: The development of ERAS (Enhanced Recovery After Surgery) protocols in patients undergoing major surgery has brought perioperative benefits in several disciplines. Its main application in urology is focused on patients undergoing radical cystectomy. OBJECTIVE: Systematic review of the available literature on ERAS protocols applied to patients undergoing radical cystectomy in terms of perioperative outcomes as well in the analysis of their implementation. EVIDENCE ACQUISITION: A bibliographic search was conducted in the electronic databases PubMed, Embase, Cochrane and Scopus, using the terms «Cystectomy», «Enhanced Recovery After Surgery» and «Fast-Track». Randomized and non-randomized studies that compared the implementation of an ERAS protocol versus a traditional protocol in patients undergoing radical cystectomy were selected. EVIDENCE SYNTHESIS: 869 articles were identified; 25 were selected for final analysis: 22 non-randomized and 3 randomized studies. No differences were observed in terms of demographic characteristics between studies. Statistically significant differences were identified in favor of the ERAS protocol: length of hospital stay, major complication rate, time to first ambulation and return of bowel function. In the analysis of protocols, a high variability was detected in the number of items and in the implementation method. CONCLUSIONS: The multidisciplinary nature and the number of items of the ERAS protocols imply a high heterogeneity in their implementation. Further randomized studies, standardized reporting and analyzing results, as well as a systematic analysis of subsequent adherence are required to increase comparability between groups.	bladder